Variant report
| Variant | rs1249813 |
|---|---|
| Chromosome Location | chr1:75862526-75862527 |
| allele | G/T |
| Outlinks | Ensembl UCSC |
- TF binding region (count:5)
- CpG islands (count:0)
- Chromatin interactive region (count:0)
- LncRNA region (count:0)
- Mature miRNA region (count: 0)
- miRNA target sites (count:0)
(count:5 , 50 per page) page:
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| No. | Transcrition factor | Chromosome Location | Cell Line | Cell type | Cell Stage | Matched TF binding sites |
|---|---|---|---|---|---|---|
| 1 | IRF1 | chr1:75862503-75862747 | K562 | blood: | n/a | chr1:75862656-75862667 chr1:75862656-75862670 chr1:75862655-75862666 chr1:75862657-75862671 chr1:75862656-75862669 chr1:75862651-75862668 chr1:75862657-75862667 chr1:75862659-75862673 chr1:75862656-75862669 chr1:75862656-75862669 chr1:75862655-75862675 chr1:75862654-75862668 chr1:75862653-75862667 |
| 2 | E2F4 | chr1:75862397-75862626 | MCF10A-Er-Src | breast: | n/a | n/a |
| 3 | FOS | chr1:75862496-75862800 | MCF10A-Er-Src | breast: | n/a | n/a |
| 4 | FOS | chr1:75862504-75862797 | MCF10A-Er-Src | breast: | n/a | n/a |
| 5 | FOS | chr1:75862357-75862811 | MCF10A-Er-Src | breast: | n/a | n/a |
| No data |
| No data |
| No data |
| No data |
| No data |
| Variant related genes | Relation type |
|---|---|
| SLC44A5 | TF binding region |
rSNPs within LD-proxies of this variant (count:17)
| rs_ID | r2[population] |
|---|---|
| rs10874314 | 0.89[JPT][hapmap] |
| rs1249804 | 0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1249808 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1249809 | 0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1249810 | 1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1249811 | 0.81[MKK][hapmap] |
| rs1249812 | 0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1249815 | 0.83[MKK][hapmap] |
| rs1249818 | 0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1249819 | 0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1249846 | 0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes] |
| rs1249849 | 0.81[MKK][hapmap] |
| rs1313031 | 0.88[AMR][1000 genomes];0.86[EUR][1000 genomes] |
| rs1313032 | 0.87[EUR][1000 genomes] |
| rs1867352 | 1.00[JPT][hapmap] |
| rs1889037 | 1.00[JPT][hapmap] |
| rs6593573 | 0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes] |
Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page:
1
| No. | Variant name | Chromosome position | Chromatin state | Related regulatory elements | Target genes | Extended variants | Associated traits |
|---|---|---|---|---|---|---|---|
| 1 | esv3368999 | chr1:75524762-75933220 | Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers | TF binding regionCpG islandChromatin interactive regionlncRNA | 8 gene(s) | inside rSNPs | diseases |
| 2 | nsv1013952 | chr1:75716654-75936048 | Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers | TF binding regionCpG islandChromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
| 3 | nsv535004 | chr1:75716654-75936048 | ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers | TF binding regionCpG islandChromatin interactive region | 3 gene(s) | inside rSNPs | diseases |
| 4 | nsv1455 | chr1:75812377-75864182 | Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription | TF binding regionCpG islandChromatin interactive region | 2 gene(s) | inside rSNPs | diseases |
| 5 | nsv519329 | chr1:75830438-76358591 | Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS | TF binding regionCpG islandChromatin interactive regionlncRNAmiRNA target site | 35 gene(s) | inside rSNPs | diseases |
mRNA abundance (count:12)
| SNP | Gene | Cis/trans | Tissue | Source |
|---|---|---|---|---|
| rs1249813 | SLC44A5 | cis | Muscle Skeletal | GTEx |
| rs1249813 | SLC44A5 | cis | Thyroid | GTEx |
| rs1249813 | SLC44A5 | cis | lesional skin | skin_eQTL |
| rs1249813 | SLC44A5 | cis | parietal | SCAN |
| rs1249813 | SLC44A5 | Cis_1M | lymphoblastoid | RTeQTL |
| rs1249813 | MSH4 | cis | parietal | SCAN |
| rs1249813 | SLC44A5 | cis | Skin Sun Exposed Lower leg | GTEx |
| rs1249813 | SLC44A5 | cis | lung | GTEx |
| rs1249813 | SLC44A5 | cis | Esophagus Mucosa | GTEx |
| rs1249813 | SLC44A5 | cis | normal skin | skin_eQTL |
| rs1249813 | SLC44A5 | cis | uninvolved skin | skin_eQTL |
| rs1249813 | SLC44A5 | cis | Heart Left Ventricle | GTEx |
Chromatin state (count:0 , 50 per page) page:
| No data |
